# HG changeset patch
# User galaxyp
# Date 1554278658 14400
# Node ID 5f49ffce52cbc25ced7061bb5e104b5df784660e

planemo upload commit be7e9677908b7864ef0b965a1e219a1840eeb2ec

diff -r 000000000000 -r 5f49ffce52cb peptide_genomic_coordinate.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_genomic_coordinate.py	Wed Apr 03 04:04:18 2019 -0400
@@ -0,0 +1,154 @@
+#!/usr/bin/env python
+# 
+# Author: Praveen Kumar
+# University of Minnesota
+#
+# Get peptide's genomic coordinate from the protein's genomic mapping sqlite file (which is derived from the https://toolshed.g2.bx.psu.edu/view/galaxyp/translate_bed/038ecf54cbec)
+# 
+# python peptideGenomicCoordinate.py <peptide_list> <mz_to_sqlite DB> <genomic mapping file DB> <output.bed>
+# 
+import sys
+import sqlite3
+
+
+def main():
+    conn = sqlite3.connect(sys.argv[2])
+    c = conn.cursor()
+    c.execute("DROP table if exists novel")
+    conn.commit()
+    c.execute("CREATE TABLE novel(peptide text)")
+    pepfile = open(sys.argv[1],"r")
+    
+    pep_seq = []
+    for seq in pepfile.readlines():
+        seq = seq.strip()
+        pep_seq.append(tuple([seq]))
+    
+    c.executemany("insert into novel(peptide) values(?)", pep_seq)
+    conn.commit()
+    
+    c.execute("SELECT distinct psm.sequence, ps.id, ps.sequence from db_sequence ps, psm_entries psm, novel n, proteins_by_peptide pbp where psm.sequence = n.peptide and pbp.peptide_ref = psm.id and pbp.id = ps.id")
+    rows = c.fetchall()
+
+    conn1 = sqlite3.connect(sys.argv[3])
+    c1 = conn1.cursor()
+
+    outfh = open(sys.argv[4], "w")
+
+    master_dict = {}
+    for each in rows:
+        peptide = each[0]
+        acc = each[1]
+        acc_seq = each[2]
+    
+        c1.execute("SELECT chrom,start,end,name,strand,cds_start,cds_end FROM feature_cds_map map WHERE map.name = '"+acc+"'")
+        coordinates = c1.fetchall()
+    
+        if len(coordinates) != 0:
+            pep_start = 0
+            pep_end = 0
+            flag = 0
+            splice_flag = 0
+            spliced_peptide = []
+            for each_entry in coordinates:
+                chromosome = each_entry[0]
+                start = int(each_entry[1])
+                end = int(each_entry[2])
+                strand = each_entry[4]
+                cds_start = int(each_entry[5])
+                cds_end = int(each_entry[6])
+                pep_pos_start = (acc_seq.find(peptide)*3)
+                pep_pos_end = pep_pos_start + (len(peptide)*3)
+                if pep_pos_start >= cds_start and pep_pos_end <= cds_end:
+                    if strand == "+":
+                        pep_start = start + pep_pos_start - cds_start
+                        pep_end = start + pep_pos_end - cds_start
+                        pep_thick_start = 0
+                        pep_thick_end = len(peptide)
+                        flag == 1
+                    else:
+                        pep_end = end - pep_pos_start + cds_start
+                        pep_start = end - pep_pos_end + cds_start
+                        pep_thick_start = 0
+                        pep_thick_end = len(peptide)
+                        flag == 1
+                    spliced_peptide = []
+                    splice_flag = 0
+                else:
+                    if flag == 0:
+                        if strand == "+":
+                            if pep_pos_start >= cds_start and pep_pos_start <= cds_end and pep_pos_end > cds_end:
+                                pep_start = start + pep_pos_start - cds_start
+                                pep_end = end
+                                pep_thick_start = 0
+                                pep_thick_end = (pep_end-pep_start)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            elif pep_pos_end >= cds_start and pep_pos_end <= cds_end and pep_pos_start < cds_start:
+                                pep_start = start
+                                pep_end = start + pep_pos_end - cds_start
+                                pep_thick_start = (len(peptide)*3)-(pep_end-pep_start)
+                                pep_thick_end = (len(peptide)*3)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            else:
+                                pass
+                        else:
+                            if pep_pos_start >= cds_start and pep_pos_start <= cds_end and pep_pos_end >= cds_end:
+                                pep_start = start
+                                pep_end = end - pep_pos_start - cds_start
+                                pep_thick_start = 0
+                                pep_thick_end = (pep_end-pep_start)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            elif pep_pos_end >= cds_start and pep_pos_end <= cds_end and pep_pos_start <= cds_start:
+                                pep_start = end - pep_pos_end + cds_start
+                                pep_end = end
+                                pep_thick_start = (len(peptide)*3)-(pep_end-pep_start)
+                                pep_thick_end = (len(peptide)*3)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            else:
+                                pass
+
+            if len(spliced_peptide) == 0:
+                if strand == "+":
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"]
+                else:
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"]
+                outfh.write("\t".join(bed_line)+"\n")
+            else:
+                if strand == "+":
+                    pep_entry = spliced_peptide
+                    pep_start = min([pep_entry[0][0], pep_entry[1][0]])
+                    pep_end = max([pep_entry[0][1], pep_entry[1][1]])
+                    blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))]
+                    blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))]
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)]
+                    outfh.write("\t".join(bed_line)+"\n")
+                else:
+                    pep_entry = spliced_peptide
+                    pep_start = min([pep_entry[0][0], pep_entry[1][0]])
+                    pep_end = max([pep_entry[0][1], pep_entry[1][1]])
+                    blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))]
+                    blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))]
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)]
+                    outfh.write("\t".join(bed_line)+"\n")
+    c.execute("DROP table novel")
+    conn.commit()
+    conn.close()
+    conn1.close()
+    outfh.close()
+    pepfile.close()
+    
+    return None
+if __name__ == "__main__":
+    main()
diff -r 000000000000 -r 5f49ffce52cb peptide_genomic_coordinate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_genomic_coordinate.xml	Wed Apr 03 04:04:18 2019 -0400
@@ -0,0 +1,58 @@
+<tool id="peptide_genomic_coordinate" name="Peptide Genomic Coodinate" version="0.1.1">
+    <description>Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB</description>
+    <requirements>
+        <requirement type="package" version="3.7.1">python</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/peptide_genomic_coordinate.py' 
+        '$peptideinput'
+        '$mzsqlite'
+        '$mapping'
+        '$peptide_bed'
+    ]]></command>
+    <inputs>
+        <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
+        <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
+        <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
+    </inputs>
+    <outputs>
+        <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="peptideinput" value="peptides.tabular"/>
+            <param name="mzsqlite" value="test_mz_to_sqlite.sqlite"/>
+            <param name="mapping" value="test_genomic_mapping_sqlite.sqlite"/>
+            <output name="peptide_bed">
+                <assert_contents>
+                    <has_text text="115176449" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **Peptide Genomic Coodinate**
+
+        Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files. This tool is useful in a proteogenomics workflow.
+        This program loads two sqlite databases (mzsqlite and genomic mapping sqlite files) and calculates the genomic coordinates of the peptides provided as input. This outputs bed file for peptides.
+    
+        Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file 
+        Output: Tabular BED file with all the columns
+        
+        
+
+    ]]></help>
+    <citations>
+      <citation type="bibtex">
+@misc{peptidegenomiccoodinate,
+    author={Kumar, Praveen},
+    year={2018},
+    title={Peptide Genomic Coordinate}
+}
+      </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 5f49ffce52cb test-data/peptides.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptides.tabular	Wed Apr 03 04:04:18 2019 -0400
@@ -0,0 +1,4 @@
+AVDPDSSAEASGLR
+DGDLENPVLYSGAVK
+DSGASGSILEASAAR
+ELGSSDLTAR
diff -r 000000000000 -r 5f49ffce52cb test-data/peptides_BED.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptides_BED.bed	Wed Apr 03 04:04:18 2019 -0400
@@ -0,0 +1,4 @@
+chr11	115176449	115176491	AVDPDSSAEASGLR	255	+	115176449	115176491	0	1	42	0
+chr5	121445444	121445489	DGDLENPVLYSGAVK	255	-	121445444	121445489	0	1	45	0
+chr17	22866997	22867042	DSGASGSILEASAAR	255	-	22866997	22867042	0	1	45	0
+chr2	91155262	91155292	ELGSSDLTAR	255	-	91155262	91155292	0	1	30	0
diff -r 000000000000 -r 5f49ffce52cb test-data/test_genomic_mapping_sqlite.sqlite
Binary file test-data/test_genomic_mapping_sqlite.sqlite has changed
diff -r 000000000000 -r 5f49ffce52cb test-data/test_mz_to_sqlite.sqlite
Binary file test-data/test_mz_to_sqlite.sqlite has changed