| Previous changeset 0:65c9ce351343 (2017-01-20) Next changeset 2:8fdd3e06e1ec (2018-06-25) |
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Commit message:
planemo upload commit 68b7e251486853b77396932b588c20f389c366d2 |
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modified:
rename.py rename_scaffold.xml |
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added:
rename_scaffold.iml test-data/Dbia3_index.csv |
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removed:
test-data/Dbia3_index.fa |
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| diff -r 65c9ce351343 -r 0d13e4410c3d rename.py --- a/rename.py Fri Jan 20 17:06:52 2017 -0500 +++ b/rename.py Mon Jun 18 18:36:00 2018 -0400 |
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| @@ -2,9 +2,10 @@ Call rename to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file """ import sys +import csv from collections import OrderedDict -def rename(inputfile, outputfile, indexfile): +def rename(inputfile, outputfile, writer): namemap = OrderedDict() with open(outputfile, 'w') as out: with open(inputfile, 'r') as rf: @@ -16,21 +17,19 @@ newname = "scaffold_" + str(i) line = ">" + newname i = i+1 - namemap[oldname] = newname + writer.writerow([oldname, newname]) #TODO: Add line breaks to chromosome sequences that are in a single line - #else: - #if (len(line) > 50): - #for out.write(line.rstrip() + "\n") - with open(indexfile, 'w') as index: - for k in namemap: - index.write(k + "\t" + namemap[k] + "\n") def main(): inputfile = str(sys.argv[1]) outputfile = str(sys.argv[2]) indexfile = str(sys.argv[3]) - rename(inputfile, outputfile, indexfile) + csvfile = open(indexfile, 'w') + fieldnames = ['Original sequence name', 'Renamed sequence name'] + writer = csv.writer(csvfile) + writer.writerow(fieldnames) + rename(inputfile, outputfile, writer) if __name__ == "__main__": main() |
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| diff -r 65c9ce351343 -r 0d13e4410c3d rename_scaffold.iml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_scaffold.iml Mon Jun 18 18:36:00 2018 -0400 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module type="PYTHON_MODULE" version="4"> + <component name="NewModuleRootManager" inherit-compiler-output="true"> + <exclude-output /> + <content url="file://$MODULE_DIR$" /> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> +</module> \ No newline at end of file |
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| diff -r 65c9ce351343 -r 0d13e4410c3d rename_scaffold.xml --- a/rename_scaffold.xml Fri Jan 20 17:06:52 2017 -0500 +++ b/rename_scaffold.xml Mon Jun 18 18:36:00 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rename_scaffold" name="rename the scaffolds" version="0.1.0"> +<tool id="rename_scaffold" name="rename the scaffolds" version="1.1"> <description>Rename the scaffolds so that they won't exceed 31 characters</description> <stdio> <exit_code range="1:" /> @@ -11,14 +11,14 @@ </inputs> <outputs> <data name="output" format="fasta" label="${tool.name} on ${on_string}: renamed_reference" /> - <data name="index" format="fasta" label="${tool.name} on ${on_string}: name mapping"/> + <data name="index" format="csv" label="${tool.name} on ${on_string}: name mapping"/> </outputs> <tests> <test> <!-- Test with Dbia3.fa --> <param name="input" value="Dbia3.fa" /> <output name="output" file="Dbia3_renamed.fa"/> - <output name="index" file="Dbia3_index.fa"/> + <output name="index" file="Dbia3_index.csv"/> </test> </tests> <help><![CDATA[ |
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| diff -r 65c9ce351343 -r 0d13e4410c3d test-data/Dbia3_index.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_index.csv Mon Jun 18 18:36:00 2018 -0400 |
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| @@ -0,0 +1,71 @@ +Original sequence name,Renamed sequence name +contig1,scaffold_1 +contig2,scaffold_2 +contig3,scaffold_3 +contig4,scaffold_4 +contig5,scaffold_5 +contig6,scaffold_6 +contig7,scaffold_7 +contig8,scaffold_8 +contig9,scaffold_9 +contig10,scaffold_10 +contig11,scaffold_11 +contig12,scaffold_12 +contig13,scaffold_13 +contig14,scaffold_14 +contig15,scaffold_15 +contig16,scaffold_16 +contig17,scaffold_17 +contig18,scaffold_18 +contig19,scaffold_19 +contig20,scaffold_20 +contig21,scaffold_21 +contig22,scaffold_22 +contig23,scaffold_23 +contig24,scaffold_24 +contig25,scaffold_25 +contig26,scaffold_26 +contig27,scaffold_27 +contig28,scaffold_28 +contig29,scaffold_29 +contig30,scaffold_30 +contig31,scaffold_31 +contig32,scaffold_32 +contig33,scaffold_33 +contig34,scaffold_34 +contig35,scaffold_35 +contig36,scaffold_36 +contig37,scaffold_37 +contig38,scaffold_38 +contig39,scaffold_39 +contig40,scaffold_40 +contig41,scaffold_41 +contig42,scaffold_42 +contig43,scaffold_43 +contig44,scaffold_44 +contig45,scaffold_45 +contig46,scaffold_46 +contig47,scaffold_47 +contig48,scaffold_48 +contig49,scaffold_49 +contig50,scaffold_50 +contig51,scaffold_51 +contig52,scaffold_52 +contig53,scaffold_53 +contig54,scaffold_54 +contig55,scaffold_55 +contig56,scaffold_56 +contig57,scaffold_57 +contig58,scaffold_58 +contig59,scaffold_59 +contig60,scaffold_60 +contig61,scaffold_61 +contig62,scaffold_62 +contig63,scaffold_63 +contig64,scaffold_64 +contig65,scaffold_65 +contig66,scaffold_66 +contig67,scaffold_67 +contig68,scaffold_68 +contig69,scaffold_69 +contig70,scaffold_70 |
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| diff -r 65c9ce351343 -r 0d13e4410c3d test-data/Dbia3_index.fa --- a/test-data/Dbia3_index.fa Fri Jan 20 17:06:52 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,70 +0,0 @@ -contig1 scaffold_1 -contig2 scaffold_2 -contig3 scaffold_3 -contig4 scaffold_4 -contig5 scaffold_5 -contig6 scaffold_6 -contig7 scaffold_7 -contig8 scaffold_8 -contig9 scaffold_9 -contig10 scaffold_10 -contig11 scaffold_11 -contig12 scaffold_12 -contig13 scaffold_13 -contig14 scaffold_14 -contig15 scaffold_15 -contig16 scaffold_16 -contig17 scaffold_17 -contig18 scaffold_18 -contig19 scaffold_19 -contig20 scaffold_20 -contig21 scaffold_21 -contig22 scaffold_22 -contig23 scaffold_23 -contig24 scaffold_24 -contig25 scaffold_25 -contig26 scaffold_26 -contig27 scaffold_27 -contig28 scaffold_28 -contig29 scaffold_29 -contig30 scaffold_30 -contig31 scaffold_31 -contig32 scaffold_32 -contig33 scaffold_33 -contig34 scaffold_34 -contig35 scaffold_35 -contig36 scaffold_36 -contig37 scaffold_37 -contig38 scaffold_38 -contig39 scaffold_39 -contig40 scaffold_40 -contig41 scaffold_41 -contig42 scaffold_42 -contig43 scaffold_43 -contig44 scaffold_44 -contig45 scaffold_45 -contig46 scaffold_46 -contig47 scaffold_47 -contig48 scaffold_48 -contig49 scaffold_49 -contig50 scaffold_50 -contig51 scaffold_51 -contig52 scaffold_52 -contig53 scaffold_53 -contig54 scaffold_54 -contig55 scaffold_55 -contig56 scaffold_56 -contig57 scaffold_57 -contig58 scaffold_58 -contig59 scaffold_59 -contig60 scaffold_60 -contig61 scaffold_61 -contig62 scaffold_62 -contig63 scaffold_63 -contig64 scaffold_64 -contig65 scaffold_65 -contig66 scaffold_66 -contig67 scaffold_67 -contig68 scaffold_68 -contig69 scaffold_69 -contig70 scaffold_70 |