UNIX for Dummies Questions & Answers

>gma-miR172a    Glyma02g28845
>gma-miR1513a-3p        Glyma02g15840
>gma-miR166a-5p Glyma02g15840
>gma-miR1530    Glyma02g15130
>gma-miR1507a   Glyma02g01841

Glyma01g07930   Glyma02g13330
Glyma01g07390   Glyma02g13120

For each gff file:
  For each line in the gff file:
    If all entries in the line are in name.txt someplace, add line to "yes" file
    Otherwise add the line to the "no" file

for file in *.gff
do
  fileprefix=`echo "$file" | sed 's/\.gff$//'`
  cat ${file} | while read line
  do
    include="yes"
    for entry in $line
    do
      grep "$entry" name.txt > /dev/null || include=""
    done
    if [ -n "$include" ]
    then
      echo "${line}" >> "${fileprefix}_yes.gff"
    else
      echo "${line}" >> "${fileprefix}_no.gff"
    fi
  done
done

#!/bin/sh

#Run the following for every file in the current directory that ends with ".gff" - note that it might
# get confused if you have gff files with a space in the filename.
for file in *.gff
do
  # Find the filename prefix by removing the ".gff" part of the filename
  fileprefix=`echo "$file" | sed 's/\.gff$//'`
  # Go through the .gff file line by line
  cat ${file} | while read line
  do
    # by default, assume we want to include all lines in the "yes" file
    include="yes"
    # For each word on the given line, see if it's present in "name.txt"
    for entry in $line
    do
      # If it is not present, then we know we need to put this line in the "no" file instead
      grep "$entry" name.txt > /dev/null || include=""
    done
    # If we get to the end and $include still has something in it ("yes") then we know we found all the entries on this line
    # So we add it to the "yes" file, otherwise the "no" file
    if [ -n "$include" ]
    then
      echo "${line}" >> "${fileprefix}_yes.gff"
    else
      echo "${line}" >> "${fileprefix}_no.gff"
    fi
  done
  # move onto the next line in the current .gff file
done
# move onto the next gff file

EXT=("YES" "NO")
for FN in *.gff
  do while read line
       do grep -Eqi "${line// /|}" name.txt
          echo "$line" >> ${FN%.gff}_${EXT[$?]}.gff
       done <"$FN"
  done