Python, Regular expression for taking a file name in a string

Question

I have a file with lines that looks like this:

chr5    153584000   153599999   D16073_orphan_reads.fa;709[F18|R11] unkn    1   unkn    2509

chr7    153764000   153775999   D16073_orphan_reads.fa;710[F9|R21],14892_orphan_reads.fa;229[F19|R16]   unkn        1   unkn    2510

chr3    127848000   127871999   B15971_orphan_reads.fa;172[F35|R6],D16157-14_orphan_reads.fa;183[F6|R13],14892_orphan_reads.fa;229[F19|R16],USP19283_orphan_reads.fa;336[F10|R6],D15927-14_orphan_reads.fa;176[F11|R10],1007,1007   46  1007    1658

(...)

I want to create a Regex that takes the fasta file (.fa) name for each line ( sometimes I have more than one file per line).

I would like to end up with something like:

D16073_orphan_reads.fa

D16073_orphan_reads.fa, 14892_orphan_reads.fa

B15971_orphan_reads.fa, D1615714_orphan_reads.fa, 14892_orphan_reads.fa,USP19283_orphan_reads.fa, D15927-14_orphan_reads.fa

I tried:

 pattern= re.search(".+.[.fa]", line)

The problem is that the file names have very irregular names. The only clues are:

-end with .fa

-start after the comma

thanks

Answer 1

The regex ([\w-]+\.fa); used in an re.findall() call will accomplish this.

import re

data = '''chr5    153584000   153599999   D16073_orphan_reads.fa;709[F18|R11] unkn    1   unkn    2509

chr7    153764000   153775999   D16073_orphan_reads.fa;710[F9|R21],14892_orphan_reads.fa;229[F19|R16]   unkn        1   unkn    2510

chr3    127848000   127871999   B15971_orphan_reads.fa;172[F35|R6],D16157-14_orphan_reads.fa;183[F6|R13],14892_orphan_reads.fa;229[F19|R16],USP19283_orphan_reads.fa;336[F10|R6],D15927-14_orphan_reads.fa;176[F11|R10],1007,1007   46  1007    1658
'''

for line in data.splitlines():
    filenames = re.findall('([\w|-]+\.fa);', line)
    if filenames:
        print ', '.join(filenames)

output:

D16073_orphan_reads.fa
D16073_orphan_reads.fa, 14892_orphan_reads.fa
B15971_orphan_reads.fa, D16157-14_orphan_reads.fa, 14892_orphan_reads.fa, USP19283_orphan_reads.fa, D15927-14_orphan_reads.fa