# HG changeset patch # User iuc # Date 1674655432 0 # Node ID 9a811adb714f6cb004b3c147284b27d9ebbc0222 # Parent 269c627ae9f442c839e64cc6536cf58bd640a99a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212 diff -r 269c627ae9f4 -r 9a811adb714f fastaregexfinder.py --- a/fastaregexfinder.py Wed Jun 20 11:06:57 2018 -0400 +++ b/fastaregexfinder.py Wed Jan 25 14:03:52 2023 +0000 @@ -1,33 +1,33 @@ #!/usr/bin/env python -import re -import sys -import string import argparse import operator +import re +import sys -VERSION='0.1.1' +VERSION = "0.1.1" -parser = argparse.ArgumentParser(description=""" +parser = argparse.ArgumentParser( + description=""" DESCRIPTION - + Search a fasta file for matches to a regex and return a bed file with the - coordinates of the match and the matched sequence itself. - + coordinates of the match and the matched sequence itself. + Output bed file has columns: 1. Name of fasta sequence (e.g. chromosome) 2. Start of the match 3. End of the match 4. ID of the match 5. Length of the match - 6. Strand + 6. Strand 7. Matched sequence as it appears on the forward strand - + For matches on the reverse strand it is reported the start and end position on the forward strand and the matched string on the forward strand (so the G4 'GGGAGGGT' present on the reverse strand is reported as ACCCTCCC). - + Note: Fasta sequences (chroms) are read in memory one at a time along with the matches for that chromosome. The order of the output is: chroms as they are found in the inut fasta, matches @@ -37,7 +37,7 @@ ## Test data: echo '>mychr' > /tmp/mychr.fa echo 'ACTGnACTGnACTGnTGAC' >> /tmp/mychr.fa - + fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG' mychr 0 4 mychr_0_4_for 4 + ACTG mychr 5 9 mychr_5_9_for 4 + ACTG @@ -47,8 +47,8 @@ mychr 0 4 mychr_0_4_for 4 + ACT[3,4] mychr 5 9 mychr_5_9_for 4 + ACT[3,4] mychr 10 14 mychr_10_14_for 4 + ACT[3,4] - - less /tmp/mychr.fa | fastaRegexFinder.py -f - -r 'A\w\wGn' + + less /tmp/mychr.fa | fastaRegexFinder.py -f - -r 'A\\w\\wGn' mychr 0 5 mychr_0_5_for 5 + ACTGn mychr 5 10 mychr_5_10_for 5 + ACTGn mychr 10 15 mychr_10_15_for 5 + ACTGn @@ -56,62 +56,78 @@ DOWNLOAD fastaRegexFinder.py is hosted at https://github.com/dariober/bioinformatics-cafe/tree/master/fastaRegexFinder - """, formatter_class= argparse.RawTextHelpFormatter) - -parser.add_argument('--fasta', '-f', - type= str, - help='''Input fasta file to search. Use '-' to read the file from stdin. - - ''', - required= True) + """, + formatter_class=argparse.RawTextHelpFormatter, +) -parser.add_argument('--regex', '-r', - type= str, - help='''Regex to be searched in the fasta input. +parser.add_argument( + "--fasta", + "-f", + type=str, + help="Input fasta file to search. Use '-' to read the file from stdin.", + required=True, +) + +parser.add_argument( + "--regex", + "-r", + type=str, + help="""Regex to be searched in the fasta input. Matches to the reverse complement will have - strand. -The default regex is '([gG]{3,}\w{1,7}){3,}[gG]{3,}' which searches -for G-quadruplexes. - ''', - default= '([gG]{3,}\w{1,7}){3,}[gG]{3,}') +The default regex is '([gG]{3,}\\w{1,7}){3,}[gG]{3,}' which searches +for G-quadruplexes.""", + default="([gG]{3,}\\w{1,7}){3,}[gG]{3,}", +) -parser.add_argument('--matchcase', '-m', - action= 'store_true', - help='''Match case while searching for matches. Default is +parser.add_argument( + "--matchcase", + "-m", + action="store_true", + help="""Match case while searching for matches. Default is to ignore case (I.e. 'ACTG' will match 'actg'). - ''') + """, +) -parser.add_argument('--noreverse', - action= 'store_true', - help='''Do not search the reverse complement of the input fasta. -Use this flag to search protein sequences. - ''') +parser.add_argument( + "--noreverse", + action="store_true", + help="""Do not search the reverse complement of the input fasta. +Use this flag to search protein sequences.""", +) -parser.add_argument('--maxstr', - type= int, - required= False, - default= 10000, - help='''Maximum length of the match to report in the 7th column of the output. +parser.add_argument( + "--maxstr", + type=int, + required=False, + default=10000, + help="""Maximum length of the match to report in the 7th column of the output. Default is to report up to 10000nt. Truncated matches are reported as [,] - ''') + """, +) -parser.add_argument('--seqnames', '-s', - type= str, - nargs= '+', - default= [None], - required= False, - help='''List of fasta sequences in --fasta to +parser.add_argument( + "--seqnames", + "-s", + type=str, + nargs="+", + default=[None], + required=False, + help="""List of fasta sequences in --fasta to search. E.g. use --seqnames chr1 chr2 chrM to search only these crhomosomes. Default is to search all the sequences in input. - ''') -parser.add_argument('--quiet', '-q', - action= 'store_true', - help='''Do not print progress report (i.e. sequence names as they are scanned). - ''') + """, +) +parser.add_argument( + "--quiet", + "-q", + action="store_true", + help="""Do not print progress report (i.e. sequence names as they are scanned). + """, +) - -parser.add_argument('--version', '-v', action='version', version='%(prog)s ' + VERSION) +parser.add_argument("--version", "-v", action="version", version="%(prog)s " + VERSION) args = parser.parse_args() @@ -119,28 +135,30 @@ " --------------------------[ Check and parse arguments ]---------------------- " if args.matchcase: - flag= 0 + flag = 0 else: - flag= re.IGNORECASE + flag = re.IGNORECASE " ------------------------------[ Functions ]--------------------------------- " + def sort_table(table, cols): - """ Code to sort list of lists + """Code to sort list of lists see http://www.saltycrane.com/blog/2007/12/how-to-sort-table-by-columns-in-python/ sort a table by multiple columns - table: a list of lists (or tuple of tuples) where each inner list + table: a list of lists (or tuple of tuples) where each inner list represents a row cols: a list (or tuple) specifying the column numbers to sort by e.g. (1,0) would sort by column 1, then by column 0 """ for col in reversed(cols): table = sorted(table, key=operator.itemgetter(col)) - return(table) + return table + def trimMatch(x, n): - """ Trim the string x to be at most length n. Trimmed matches will be reported + """Trim the string x to be at most length n. Trimmed matches will be reported with the syntax ACTG[a,b] where Ns are the beginning of x, a is the length of the trimmed strng (e.g 4 here) and b is the full length of the match EXAMPLE: @@ -150,105 +168,114 @@ >>>'ACTGNNNN' """ if len(x) > n and n is not None: - m= x[0:n] + '[' + str(n) + ',' + str(len(x)) + ']' + m = x[0:n] + "[" + str(n) + "," + str(len(x)) + "]" else: - m= x - return(m) + m = x + return m + def revcomp(x): """Reverse complement string x. Ambiguity codes are handled and case conserved. - + Test x= 'ACGTRYSWKMBDHVNacgtryswkmbdhvn' revcomp(x) """ - compdict= {'A':'T', - 'C':'G', - 'G':'C', - 'T':'A', - 'R':'Y', - 'Y':'R', - 'S':'W', - 'W':'S', - 'K':'M', - 'M':'K', - 'B':'V', - 'D':'H', - 'H':'D', - 'V':'B', - 'N':'N', - 'a':'t', - 'c':'g', - 'g':'c', - 't':'a', - 'r':'y', - 'y':'r', - 's':'w', - 'w':'s', - 'k':'m', - 'm':'k', - 'b':'v', - 'd':'h', - 'h':'d', - 'v':'b', - 'n':'n'} - xrc= [] + compdict = { + "A": "T", + "C": "G", + "G": "C", + "T": "A", + "R": "Y", + "Y": "R", + "S": "W", + "W": "S", + "K": "M", + "M": "K", + "B": "V", + "D": "H", + "H": "D", + "V": "B", + "N": "N", + "a": "t", + "c": "g", + "g": "c", + "t": "a", + "r": "y", + "y": "r", + "s": "w", + "w": "s", + "k": "m", + "m": "k", + "b": "v", + "d": "h", + "h": "d", + "v": "b", + "n": "n", + } + xrc = [] for n in x: xrc.append(compdict[n]) - xrc= ''.join(xrc)[::-1] - return(xrc) + xrc = "".join(xrc)[::-1] + return xrc + + # ----------------------------------------------------------------------------- -psq_re_f= re.compile(args.regex, flags= flag) -## psq_re_r= re.compile(regexrev) +psq_re_f = re.compile(args.regex, flags=flag) +# psq_re_r= re.compile(regexrev) -if args.fasta != '-': - ref_seq_fh= open(args.fasta) +if args.fasta != "-": + ref_seq_fh = open(args.fasta) else: - ref_seq_fh= sys.stdin + ref_seq_fh = sys.stdin -ref_seq=[] -line= (ref_seq_fh.readline()).strip() -chr= re.sub('^>', '', line) -line= (ref_seq_fh.readline()).strip() -gquad_list= [] +ref_seq = [] +line = (ref_seq_fh.readline()).strip() +chr = re.sub("^>", "", line) +line = (ref_seq_fh.readline()).strip() +gquad_list = [] while True: if not args.quiet: - sys.stderr.write('Processing %s\n' %(chr)) - while line.startswith('>') is False: + sys.stderr.write("Processing %s\n" % (chr)) + while line.startswith(">") is False: ref_seq.append(line) - line= (ref_seq_fh.readline()).strip() - if line == '': + line = (ref_seq_fh.readline()).strip() + if line == "": break - ref_seq= ''.join(ref_seq) + ref_seq = "".join(ref_seq) if args.seqnames == [None] or chr in args.seqnames: for m in re.finditer(psq_re_f, ref_seq): - matchstr= trimMatch(m.group(0), args.maxstr) - quad_id= str(chr) + '_' + str(m.start()) + '_' + str(m.end()) + '_for' - gquad_list.append([chr, m.start(), m.end(), quad_id, len(m.group(0)), '+', matchstr]) + matchstr = trimMatch(m.group(0), args.maxstr) + quad_id = str(chr) + "_" + str(m.start()) + "_" + str(m.end()) + "_for" + gquad_list.append( + [chr, m.start(), m.end(), quad_id, len(m.group(0)), "+", matchstr] + ) if args.noreverse is False: - ref_seq= revcomp(ref_seq) - seqlen= len(ref_seq) + ref_seq = revcomp(ref_seq) + seqlen = len(ref_seq) for m in re.finditer(psq_re_f, ref_seq): - matchstr= trimMatch(revcomp(m.group(0)), args.maxstr) - mstart= seqlen - m.end() - mend= seqlen - m.start() - quad_id= str(chr) + '_' + str(mstart) + '_' + str(mend) + '_rev' - gquad_list.append([chr, mstart, mend, quad_id, len(m.group(0)), '-', matchstr]) - gquad_sorted= sort_table(gquad_list, (1,2,3)) - gquad_list= [] + matchstr = trimMatch(revcomp(m.group(0)), args.maxstr) + mstart = seqlen - m.end() + mend = seqlen - m.start() + quad_id = str(chr) + "_" + str(mstart) + "_" + str(mend) + "_rev" + gquad_list.append( + [chr, mstart, mend, quad_id, len(m.group(0)), "-", matchstr] + ) + gquad_sorted = sort_table(gquad_list, (1, 2, 3)) + gquad_list = [] for xline in gquad_sorted: - xline= '\t'.join([str(x) for x in xline]) + xline = "\t".join([str(x) for x in xline]) print(xline) - chr= re.sub('^>', '', line) - ref_seq= [] - line= (ref_seq_fh.readline()).strip() - if line == '': + chr = re.sub("^>", "", line) + ref_seq = [] + line = (ref_seq_fh.readline()).strip() + if line == "": break -#gquad_sorted= sort_table(gquad_list, (0,1,2,3)) +# gquad_sorted= sort_table(gquad_list, (0,1,2,3)) # -#for line in gquad_sorted: +# for line in gquad_sorted: # line= '\t'.join([str(x) for x in line]) # print(line) sys.exit() diff -r 269c627ae9f4 -r 9a811adb714f fastaregexfinder.xml --- a/fastaregexfinder.xml Wed Jun 20 11:06:57 2018 -0400 +++ b/fastaregexfinder.xml Wed Jan 25 14:03:52 2023 +0000 @@ -1,14 +1,15 @@ - + Search in fasta for regexp match + python - python $__tool_directory__/fastaregexfinder.py --version + python '$__tool_directory__/fastaregexfinder.py' --version $output +> '$output' ]]>